X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSelenomethionine enriched DesVI model from MAD phasing

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6277PEG 5000 monomethyl ether, NaCl, S-adenosylmethionine, UDP-benzene, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8757.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.17α = 90
b = 56.096β = 92.5
c = 116.482γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montel optics2007-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
123089.80.0849.42.74049036362
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.176.50.2542.61.95470

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMAD, MRTHROUGHOUTSelenomethionine enriched DesVI model from MAD phasing2304049036362361889.80.1690.1690.1650.254random18.391
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
t_angle_deg2
t_bond_d0.01
t_gen_planes0.007
t_trig_c_planes0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3718
Nucleic Acid Atoms
Solvent Atoms544
Heterogen Atoms120

Software

Software
Software NamePurpose
SAINTdata scaling
PHASERphasing
SOLVEphasing
DMphasing
TNTrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SADABSdata scaling